Merge pull request JCSDA#1321 from climbfuji/feature/merge_rel180_int…

…o_develop

Merge release/1.8.0 into develop

.github/workflows/ubuntu-ci-containers-x86_64.yaml

@@ -8,7 +8,7 @@ on:
   #    - '**.md'
   #    - '.github/ISSUE_TEMPLATE/*'
   #    - '.gitignore'
-  # 
+  #
   schedule:
     - cron: '0 8 * * *'
   workflow_dispatch:

configs/common/packages.yaml

@@ -75,8 +75,9 @@ packages:
     # Pin version to avoid duplicates
     require: '@2.6.4'
   fms:
-    require: '@2024.02'
-    variants: 'precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io'
+    require:
+    - '@2024.02'
+    - 'precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io'
   fontconfig:
     require: '+pic'
   freetype:
@@ -214,6 +215,9 @@ packages:
   ## To avoid duplicate packages
   #py-jinja2:
   #  require: '@3.1.2'
+  # https://github.com/JCSDA/spack-stack/issues/1276
+  py-matplotlib:
+     require: '@3.7.4'
   py-meson-python:
      require: '@0.15.0'
   # Comment out for now until build problems are solved
@@ -226,9 +230,10 @@ packages:
     require: '@1.5.8 ~mpi'
   # py-numpy@1.26 causes many build problems with older Python packages
   # also check Nautilus site config when making changes here
+  # https://github.com/JCSDA/spack-stack/issues/1276
   py-numpy:
     require:
-    - '@:1.25'
+    - '@:1.23.5'
   py-pandas:
     require: '+excel'
   py-pybind11:
@@ -273,7 +278,8 @@ packages:
   w3nco:
     require: '@2.4.1'
   wgrib2:
-    require: '@3.1.1'
+    require:
+    - '@3.1.1'
   wrf-io:
     require: '@1.2.0'
   zstd:

configs/common/packages_aocc.yaml

@@ -0,0 +1,15 @@
+packages:
+  all:
+    providers:
+      blas: [openblas]
+      fftw-api: [fftw]
+      lapack: [openblas]
+  ectrans:
+    require:
+    - '~mkl +fftw'
+  gsibec:
+    require:
+    - '~mkl'
+  py-numpy:
+    require:
+    - '^openblas'

configs/containers/docker-ubuntu-clang-mpich.yaml

@@ -42,12 +42,6 @@ spack:
       externals:
       - spec: gcc-runtime@12.3.0
         prefix: /usr
-    g2:
-      # https://github.com/NOAA-EMC/NCEPLIBS-g2/issues/745
-      require:
-        - any_of: ['fflags="-fno-range-check"']
-          when: "@3.5.1 %clang"
-          message: "Extra g2 compile options for version 3.5.1 with clang"
     g2tmpl:
       # https://github.com/JCSDA/spack-stack/issues/525
       require:

configs/containers/docker-ubuntu-gcc-openmpi.yaml

@@ -45,12 +45,6 @@ spack:
       externals:
       - spec: gmake@4.3
         prefix: /usr
-    g2:
-      # https://github.com/NOAA-EMC/NCEPLIBS-g2/issues/745
-      require:
-      - any_of: ['fflags="-fno-range-check"']
-        when: "@3.5.1 %gcc"
-        message: "Extra g2 compile options for version 3.5.1 with gcc/gfortran"
     diffutils:
       buildable: false
       externals:

configs/containers/specs/jedi-ci.yaml

@@ -38,7 +38,7 @@
     py-f90nml@1.4.3,
     py-gitpython@3.1.40,
     py-h5py@3.11.0,
-    py-numpy@1.25.2,
+    py-numpy@1.23.5,
     py-pandas@1.5.3,
     py-pip,
     py-pyyaml@6.0,

configs/sites/tier1/acorn/compilers.yaml

@@ -6,18 +6,17 @@ compilers:
       cxx: CC
       f77: ftn
       fc: ftn
-    flags: {}
+    flags:
+      cflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      cxxflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      fflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
     operating_system: sles15
     modules:
-    - PrgEnv-intel/8.3.3
-    - craype/2.7.13
+    - PrgEnv-intel/8.5.0
+    - craype/2.7.17
     - intel/19.1.3.304
     - libfabric
     environment:
-      prepend_path:
-        PATH: /opt/cray/pe/gcc/10.2.0/bin
-        LD_LIBRARY_PATH: /opt/cray/pe/gcc/10.2.0/snos/lib64
-        CPATH: /opt/cray/pe/gcc/10.2.0/snos/include
       set:
         # OpenSUSE on WCOSS2 machines sets CONFIG_SITE so 
         # Automake-based builds are installed in lib64 
@@ -31,11 +30,14 @@ compilers:
       cxx: CC
       f77: ftn
       fc: ftn
-    flags: {}
+    flags:
+      cflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      cxxflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      fflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
     operating_system: sles15
     modules:
-    - PrgEnv-intel/8.3.3
-    - craype/2.7.13
+    - PrgEnv-intel/8.5.0
+    - craype/2.7.17
     - intel-classic/2022.2.0.262
     - libfabric
     environment:

configs/sites/tier1/acorn/packages.yaml

@@ -9,11 +9,6 @@
       externals:
       - spec: git-lfs@2.11.0
         modules: [git-lfs/2.11.0]
-    perl:
-      buildable: false
-      externals:
-      - spec: perl@5.26.1~cpanm+shared+threads
-        prefix: /usr
     mysql:
       buildable: false
       externals:
@@ -38,6 +33,7 @@
     gdal:
       variants: ~curl
     flex:
+      buildable: false
       externals:
       - spec: flex@2.6.4+lex
         prefix: /usr

configs/sites/tier1/acorn/packages_intel.yaml

@@ -31,21 +31,29 @@
       - '@1.2.1 ~mkl'
     py-numpy:
       require::
-      - '@:1.25 ^openblas'
+      - '^[virtuals=lapack,blas] openblas'
+      - '@:1.25'
+      - any_of: ['@:1.24']
+        when: '%intel@19.1.3.304'
     # *DH
     eckit:
       require:
       - any_of: ["@1.23.1"]
         when: "%intel@19.1.3.304"
     eccodes:
       require:
-      - any_of: ["@2.27.0"]
+      - any_of: ["@2.25.0"]
         when: "%intel@19.1.3.304"
+        message: "2.25.0 is the last version to use C++11 (as opposed to C++17)"
     py-scipy:
       require:
       - any_of: ["@1.10.1"]
         when: "%intel@19.1.3.304"
     cdo:
       require:
+      - any_of: ["@2.3.0"]
+        when: "%intel@2022.0.2.262"
+        message: "2.3.0 is the last version to use C++17"
       - any_of: ["@2.0.5"]
         when: "%intel@19.1.3.304"
+        message: "2.0.5 is the last version to use C++14"

configs/sites/tier1/atlantis/compilers.yaml

@@ -54,4 +54,3 @@ compilers:
       append_path:
         CPATH: /cm/shared/apps/intel/oneapi-2024.2.1/compiler/2024.2/opt/compiler/include/intel64/
     extra_rpaths: []
-# Todo: Define gcc compiler (default for Atlantis) for Intel (ecflow)

configs/sites/tier1/atlantis/modules.yaml

@@ -6,5 +6,3 @@ modules:
       include:
       # List of packages for which we need modules that are blacklisted by default
       - python
-      exclude:
-      - ecflow

configs/sites/tier1/atlantis/packages_oneapi.yaml

@@ -2,12 +2,12 @@ packages:
   all:
     compiler:: [oneapi@2024.2.1,gcc@11.2.0]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.13.0]
+      mpi:: [intel-oneapi-mpi@2021.13]
   mpi:
     buildable: False
   intel-oneapi-mpi:
     externals:
-    - spec: intel-oneapi-mpi@2021.13%2024.2.1
+    - spec: intel-oneapi-mpi@2021.13%oneapi@2024.2.1
       prefix: /cm/shared/apps/intel/oneapi-2024.2.1
       modules:
       - mpi/2021.13

configs/sites/tier1/aws-pcluster/README.md

@@ -116,7 +116,7 @@ apt install -y \
     liblcms2-dev \
     liblcms2-2
 
-# Install QT5 for ecflow
+# Install QT5, needed for install of ecflow
 apt install -y \
     qtcreator \
     qtbase5-dev \
@@ -217,51 +217,7 @@ sudo usermod -aG docker $USER
 exit
 ```
 
-4. Build ecflow outside of spack to be able to link against OS boost
-```
-mkdir -p /home/ubuntu/jedi/ecflow-5.8.4/src
-cd /home/ubuntu/jedi/ecflow-5.8.4/src
-wget https://github.com/ecmwf/ecflow/archive/refs/tags/5.8.4.tar.gz
-tar -xvzf 5.8.4.tar.gz
-export WK=/home/ubuntu/jedi/ecflow-5.8.4/src/ecflow-5.8.4
-export BOOST_ROOT=/usr
-
-# Build ecFlow
-cd $WK
-mkdir build
-cd build
-cmake .. -DPython3_EXECUTABLE=/usr/bin/python3 -DENABLE_STATIC_BOOST_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/home/ubuntu/jedi/ecflow-5.8.4 2>&1 | tee log.cmake
-make -j10 2>&1 | tee log.make
-make install 2>&1 | tee log.install
-
-# Create a modulefiles directory and the "ecflow/5.8.4" module file.
-mkdir -p /home/ubuntu/jedi/modulefiles/ecflow
-
-cat << 'EOF' > /home/ubuntu/jedi/modulefiles/ecflow/5.8.4
-#%Module1.0
-
-module-whatis "Provides an ecflow-5.8.4 server+ui installation for use with spack."
-
-conflict ecflow
-
-proc ModulesHelp { } {
-puts stderr "Provides an ecflow-5.8.4 server+ui installation for use with spack."
-}
-
-# Set this value
-set ECFLOW_PATH "/home/ubuntu/jedi/ecflow-5.8.4"
-
-prepend-path PATH "${ECFLOW_PATH}/bin"
-prepend-path LD_LIBRARY_PATH "${ECFLOW_PATH}/lib"
-prepend-path LIBRARY_PATH "${ECFLOW_PATH}/lib"
-prepend-path CPATH "${ECFLOW_PATH}/include"
-prepend-path CMAKE_PREFIX_PATH "${ECFLOW_PATH}"
-prepend-path PYTHONPATH "${ECFLOW_PATH}/lib/python3.10/site-packages"
-EOF
-
-```
-
-5. Install lmod. This step must be done as `root`.
+4. Install lmod. This step must be done as `root`.
 ```
 # Install lua/lmod manually because apt only has older versions
 # that are not compatible with the modern lua modules spack produces
@@ -343,7 +299,7 @@ module purge
 module list
 ```
 
-6. Install msql community server
+5. Install msql community server
 ```
 cd /home/ubuntu/jedi
 mkdir -p mysql-8.0.31/src
@@ -365,7 +321,7 @@ exit
 rm *.deb
 ```
 
-7. Option 1: Testing existing site config in spack-stack (skip steps
+6. Option 1: Testing existing site config in spack-stack (skip steps
 8-9 afterwards) this install is done directly on the NFS drive. If you are
 testing an update to the configuration, do this on the faster EBS volume (use a
 directory in /home/ubuntu) in order to ensure a faster build. Once you have
@@ -398,7 +354,7 @@ spack module lmod refresh
 spack stack setup-meta-modules
 ```
 
-8. Option 2: Test configuring site from scratch
+7. Option 2: Test configuring site from scratch
 ```
 mkdir -p /home/ubuntu/jedi && cd /home/ubuntu/jedi
 git clone -b develop --recursive https://github.com/jcsda/spack-stack spack-stack
@@ -450,15 +406,6 @@ cat << 'EOF' >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
       prefix: /usr
 EOF
 
-# Add external ecflow
-cat << 'EOF' >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
-  ecflow:
-    buildable: False
-    externals:
-    - spec: ecflow@5.8.4 +ui
-      prefix: /home/ubuntu/jedi/ecflow-5.8.4
-EOF
-
 spack compiler find --scope system
 
 export -n SPACK_SYSTEM_CONFIG_PATH
@@ -479,12 +426,12 @@ spack config add "packages:all:compiler:[intel@2021.10.0, gcc@11.4.0]"
 #         I_MPI_PMI_LIBRARY: '/opt/slurm/lib/libpmi.so'
 ```
 
-9. Option 2: To avoid duplicate library versions edit ``envs/unified-dev/site/packages.yaml``
+8. Option 2: To avoid duplicate library versions edit ``envs/unified-dev/site/packages.yaml``
 and remove entries for meson, ninja, hdf5, cmake and remove the external
 `cmake` and `openssl` entries.
 
 
-10. Concretize and install
+9. Concretize and install
 ```
 spack concretize 2>&1 | tee log.concretize.unified-env.001
 ./util/show_duplicate_packages.py -d log.concretize.unified-env.001
@@ -493,7 +440,7 @@ spack module lmod refresh
 spack stack setup-meta-modules
 ```
 
-11. Test spack-stack installation using your favorite application.
+10. Test spack-stack installation using your favorite application.
 
 ```
 # Example given for building jedi-bundle
@@ -515,12 +462,12 @@ make -j10
 ctest
 ```
 
-12. (Optional) Remove test installs of spack-stack environments, if desired.
+11. (Optional) Remove test installs of spack-stack environments, if desired.
 
-13. Create the AMI for use in the AWS parallelcluster config. You can follow
+12. Create the AMI for use in the AWS parallelcluster config. You can follow
 the official instructions for [Modifying an AWS ParallelCluster AMI](https://docs.aws.amazon.com/parallelcluster/latest/ug/building-custom-ami-v3.html#modify-an-aws-parallelcluster-ami-v3)
 
-14. Use the install to build
+13. Use the install to build
 
 ```
 # Load the intel toolchain into your environment.
@@ -551,7 +498,7 @@ make -j10
 ctest
 ```
 
-15. Once the parallel cluster head node image is fully configured and tested you
+14. Once the parallel cluster head node image is fully configured and tested you
 can create an AMI snapshot based on the configured instance using the
 [instructions](https://docs.aws.amazon.com/parallelcluster/latest/ug/building-custom-ami-v3.html)
 published by AWS. Included here is a short summary of those instructions.

configs/sites/tier1/aws-pcluster/modules.yaml

@@ -5,5 +5,3 @@ modules:
     lmod:
       include:
       - python
-      exclude:
-      - ecflow

configs/sites/tier1/aws-pcluster/packages.yaml

@@ -19,11 +19,6 @@ packages:
     externals:
     - spec: diffutils@3.8
       prefix: /usr
-  ecflow:
-    buildable: False
-    externals:
-    - spec: ecflow@5.8.4+ui+static_boost
-      prefix: /home/ubuntu/jedi/ecflow-5.8.4
   findutils:
     externals:
     - spec: findutils@4.8.0